Module pdb

PDB parsing class

This module parses PDBs in accordance to PDB Format Description Version 2.2 (1996); it is not very forgiving. Each class in this module corresponds to a record in the PDB Format Description. Much of the documentation for the classes is taken directly from the above PDB Format Description.

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PDB2PQR -- An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations

Nathan A. Baker (baker@biochem.wustl.edu) Todd Dolinsky (todd@ccb.wustl.edu) Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology Washington University in St. Louis

Jens Nielsen (Jens.Nielsen@ucd.ie) University College Dublin

Additional contributing authors listed in documentation and supporting package licenses.

Copyright (c) 2003-2007. Washington University in St. Louis. All Rights Reserved.

This file is part of PDB2PQR.

PDB2PQR is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

PDB2PQR is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with PDB2PQR; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

 If the ATOM/HETATM is not column-formatted, try to get some
 information by parsing whitespace from the right.  Look for
 five floating point numbers followed by the residue number.

 Parameters
     line:  The line to parse(string)
if record == ATOM:
     self.serial = int(string.strip(line[6:11]))
     self.name = string.strip(line[12:16])
     self.altLoc = string.strip(line[16])
     self.resName = string.strip(line[17:20])
     self.chainID = string.strip(line[21])
     self.resSeq = int(string.strip(line[22:26]))
     self.iCode = string.strip(line[26])
     self.x = float(string.strip(line[30:38]))
     self.y = float(string.strip(line[38:46]))
     self.z = float(string.strip(line[46:54]))
     try:
         self.occupancy = float(string.strip(line[54:60]))
         self.tempFactor = float(string.strip(line[60:66]))
         self.segID = string.strip(line[72:76])
         self.element = string.strip(line[76:78])
         self.charge = string.strip(line[78:80])
     except ValueError, IndexError:
         self.occupancy = 0.00
         self.tempFactor = 0.00
         self.segID = 0
         self.element = 0
         self.charge = 0
 else: raise ValueError, record

Parse PDB-format data into array of Atom objects.
Parameters
  file:  open file object 
Returns (dict, errlist)
  dict:  a dictionary indexed by PDB record names 
  errlist:  a list of record names that couldn't be parsed 

Download a random PDB and return the path name.
Returns
  path name of downloaded file